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PDXDC1 pyridoxal dependent decarboxylase domain containing 1 [ Homo sapiens (human) ]

Gene ID: 23042, updated on 3-Apr-2024

Summary

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Official Symbol
PDXDC1provided by HGNC
Official Full Name
pyridoxal dependent decarboxylase domain containing 1provided by HGNC
Primary source
HGNC:HGNC:28995
See related
Ensembl:ENSG00000179889 MIM:614244; AllianceGenome:HGNC:28995
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LP8165
Summary
Enables cadherin binding activity. Predicted to be involved in carboxylic acid metabolic process. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 42.5), duodenum (RPKM 33.1) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See PDXDC1 in Genome Data Viewer
Location:
16p13.11
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (14974735..15153218)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (14975789..15144257)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (15068592..15233267)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene PKD1P3-NPIPA1 readthrough Neighboring gene polycystin 1, transient receptor potential channel interacting pseudogene 3 Neighboring gene microRNA 6770-1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15041221-15041722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15041723-15042222 Neighboring gene nuclear pore complex interacting protein family member A1 Neighboring gene Sharpr-MPRA regulatory region 4661 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15068201-15068964 Neighboring gene KIAA2013 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr16:15106867-15106972 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15109763-15110264 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15110265-15110764 Neighboring gene microRNA 1972-1 Neighboring gene Sharpr-MPRA regulatory region 1947 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15121593-15122216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15120969-15121592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15122498-15123030 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:15149302-15149486 Neighboring gene MPRA-validated peak2507 silencer Neighboring gene N-terminal asparagine amidase Neighboring gene RRN3 homolog, RNA polymerase I transcription factor Neighboring gene Sharpr-MPRA regulatory region 13846 Neighboring gene uncharacterized LOC100505915 Neighboring gene PKD1P6-NPIPP1 readthrough Neighboring gene nuclear pore complex interacting protein pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15231552-15232159 Neighboring gene microRNA 6511b-2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:15240089-15241062 Neighboring gene polycystin 1, transient receptor potential channel interacting pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15243079-15243774 Neighboring gene microRNA 3180-4 Neighboring gene uncharacterized LOC105371096

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Genome-wide analysis of high-risk primary brain cancer pedigrees identifies PDXDC1 as a candidate brain cancer predisposition gene. Cannon-Albright LA, et al. Neuro Oncol, 2021 Feb 25. PMID 32644145, Free PMC Article
  2. Pdxdc1 modulates prepulse inhibition of acoustic startle in the mouse. Feldcamp LA, et al. Transl Psychiatry, 2017 May 9. PMID 28485732, Free PMC Article
  3. Proteome-wide Identification of HtrA2/Omi Substrates. Vande Walle L, et al. J Proteome Res, 2007 Mar. PMID 17266347
  4. Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium. Lemaitre RN, et al. PLoS Genet, 2011 Jul. PMID 21829377, Free PMC Article
  5. A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci. Okada Y, et al. Hum Mol Genet, 2010 Jun 1. PMID 20189936

See all (63) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
EBI GWAS Catalog
An atlas of genetic influences on human blood metabolites.
EBI GWAS Catalog
Discovery and refinement of loci associated with lipid levels.
EBI GWAS Catalog
Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
EBI GWAS Catalog
Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
EBI GWAS Catalog
Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.
EBI GWAS Catalog
Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
EBI GWAS Catalog
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
EBI GWAS Catalog
Human metabolic individuality in biomedical and pharmaceutical research.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0251

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cadherin binding HDA PubMed 
enables carboxy-lyase activity IEA
Inferred from Electronic Annotation
more info
  
enables pyridoxal phosphate binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in carboxylic acid metabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
is_active_in intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
pyridoxal-dependent decarboxylase domain-containing protein 1
NP_001272373.1
NP_001272374.1
NP_001272376.1
NP_001272377.1
NP_001272378.1
NP_001272379.1
NP_001310948.1
NP_001310949.1
NP_001310950.1
NP_055842.2
XP_006720928.2
XP_016878548.1
XP_016878549.1
XP_016878550.1
XP_016878552.1
XP_016878554.1
XP_024305962.1
XP_024305963.2
XP_024305965.1
XP_047289744.1
XP_047289745.1
XP_047289746.1
XP_047289747.1
XP_054185029.1
XP_054185030.1
XP_054185031.1
XP_054185032.1
XP_054185033.1
XP_054185034.1
XP_054185035.1
XP_054185036.1
XP_054185037.1
XP_054185038.1
XP_054185039.1
XP_054185040.1
XP_054185041.1
XP_054185042.1
XP_054185043.1
XP_054185044.1
XP_054185045.1
XP_054235801.1
XP_054235802.1
XP_054235803.1
XP_054235804.1
XP_054235805.1
XP_054235806.1
XP_054235807.1
XP_054235808.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001285444.2 → NP_001272373.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001272373.1

    Status: VALIDATED

    Source sequence(s)
    AC138932, BC042104, BC053946, BC060871, BM997114, BX647809, HY036748
    Consensus CDS
    CCDS66954.1
    UniProtKB/TrEMBL
    B4DHL7
    Related
    ENSP00000455070.1, ENST00000569715.5
    Conserved Domains (1) summary
    cl18945
    Location:145 → 367
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  2. NM_001285445.2 → NP_001272374.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC138932, AK299111, BC042104, BC053946, BC060871, BM997114, D87438, HY036748
    Consensus CDS
    CCDS66955.1
    UniProtKB/TrEMBL
    B4DHL7
    Related
    ENSP00000486662.1, ENST00000627450.2
    Conserved Domains (1) summary
    cl18945
    Location:144 → 366
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  3. NM_001285447.1 → NP_001272376.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 4

    See identical proteins and their annotated locations for NP_001272376.1

    Status: VALIDATED

    Source sequence(s)
    AK295168, BC033748, BC042104, BC060871, BM997114, DA775396
    UniProtKB/TrEMBL
    B4DHL7
    Related
    ENSP00000454791.1, ENST00000563679.5
    Conserved Domains (1) summary
    cl18945
    Location:157 → 379
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  4. NM_001285448.1 → NP_001272377.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AK299799, BC042104, BC060871, BM997114, DA321929
    Consensus CDS
    CCDS66957.1
    UniProtKB/TrEMBL
    B4DHL7
    Related
    ENSP00000391147.3, ENST00000450288.3
    Conserved Domains (1) summary
    cl18945
    Location:81 → 303
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  5. NM_001285449.2 → NP_001272378.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 6

    See identical proteins and their annotated locations for NP_001272378.1

    Status: VALIDATED

    Source sequence(s)
    AC139256, BC045554, CD370048
    Consensus CDS
    CCDS73830.1
    UniProtKB/Swiss-Prot
    A8K9Z5, Q6P474
    UniProtKB/TrEMBL
    Q86XE2
    Related
    ENSP00000437835.2, ENST00000535621.6
    Conserved Domains (1) summary
    cl18945
    Location:172 → 394
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  6. NM_001285450.2 → NP_001272379.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC138932, BC033748, BC053946, CA423507, HY036748
    Consensus CDS
    CCDS73831.1
    UniProtKB/Swiss-Prot
    A8K9Z5, Q6P474
    Related
    ENSP00000406703.2, ENST00000455313.6
    Conserved Domains (1) summary
    cl18945
    Location:172 → 371
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  7. NM_001324019.2 → NP_001310948.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC138932
    UniProtKB/TrEMBL
    B4DHL7

  8. NM_001324020.2 → NP_001310949.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC138932, AC139256
    UniProtKB/Swiss-Prot
    A8K9Z5, Q6P474

  9. NM_001324021.2 → NP_001310950.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 10

    Status: VALIDATED

    Source sequence(s)
    AC138932, AC139256
    UniProtKB/Swiss-Prot
    A8K9Z5, Q6P474

  10. NM_015027.4 → NP_055842.2  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_055842.2

    Status: VALIDATED

    Source sequence(s)
    AC138932, AY203955, BC042104, BC060871, BM997114, DB019664
    Consensus CDS
    CCDS32393.1
    UniProtKB/Swiss-Prot
    B4DR55, B4DSL3, E7EMH5, E7EPL4, H3BNZ1, O00236, Q4F6X7, Q6P996, Q6PID7, Q86YF1, Q8N4Q9, Q8TBS5
    UniProtKB/TrEMBL
    B4DHL7
    Related
    ENSP00000379691.4, ENST00000396410.9
    Conserved Domains (1) summary
    cl18945
    Location:172 → 394
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    14974735..15153218
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024450194.2 → XP_024305962.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X7

    UniProtKB/Swiss-Prot
    A8K9Z5, Q6P474
    Conserved Domains (1) summary
    cl18945
    Location:157 → 379
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  2. XM_017023065.2 → XP_016878554.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X6

    UniProtKB/Swiss-Prot
    A8K9Z5, Q6P474

  3. XM_047433790.1 → XP_047289746.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X8

  4. XM_024450195.2 → XP_024305963.2  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X6

  5. XM_017023059.2 → XP_016878548.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    B4DHL7
    Conserved Domains (1) summary
    cl18945
    Location:157 → 379
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  6. XM_047433788.1 → XP_047289744.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X2

  7. XM_006720865.3 → XP_006720928.2  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    B4DHL7
    Conserved Domains (1) summary
    cl18945
    Location:130 → 352
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  8. XM_017023063.2 → XP_016878552.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X4

    UniProtKB/TrEMBL
    B4DHL7

  9. XM_017023060.2 → XP_016878549.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X3

    UniProtKB/TrEMBL
    B4DHL7
    Conserved Domains (1) summary
    cl18945
    Location:181 → 403
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  10. XM_047433789.1 → XP_047289745.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X5

  11. XM_047433791.1 → XP_047289747.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X9

  12. XM_017023061.3 → XP_016878550.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    B4DHL7
    Conserved Domains (1) summary
    cl18945
    Location:157 → 379
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

  13. XM_024450197.2 → XP_024305965.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X8

    UniProtKB/Swiss-Prot
    A8K9Z5, Q6P474
    Conserved Domains (1) summary
    cl18945
    Location:130 → 352
    AAT_I; Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the ...

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187607.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    508761..694938 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329064.1 → XP_054185039.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X17

  2. XM_054329066.1 → XP_054185041.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X16

  3. XM_054329065.1 → XP_054185040.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X18

  4. XM_054329063.1 → XP_054185038.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X16

  5. XM_054329068.1 → XP_054185043.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X20

  6. XM_054329067.1 → XP_054185042.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X19

  7. XM_054329070.1 → XP_054185045.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X18

  8. XM_054329058.1 → XP_054185033.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X10

  9. XM_054329055.1 → XP_054185030.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X10

  10. XM_054329054.1 → XP_054185029.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

  11. XM_054329057.1 → XP_054185032.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X12

  12. XM_054329056.1 → XP_054185031.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X11

  13. XM_054329059.1 → XP_054185034.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

  14. XM_054329069.1 → XP_054185044.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X21

  15. XM_054329060.1 → XP_054185035.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X13

  16. XM_054329062.1 → XP_054185037.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X15

  17. XM_054329061.1 → XP_054185036.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X14

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    14975789..15144257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054379826.1 → XP_054235801.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

  2. XM_054379827.1 → XP_054235802.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X2

  3. XM_054379829.1 → XP_054235804.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X2

  4. XM_054379831.1 → XP_054235806.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X4

  5. XM_054379828.1 → XP_054235803.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X3

  6. XM_054379832.1 → XP_054235807.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X5

  7. XM_054379833.1 → XP_054235808.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X22

  8. XM_054379830.1 → XP_054235805.1  pyridoxal-dependent decarboxylase domain-containing protein 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6P996.2 GenPept UniProtKB/Swiss-Prot:Q6P996

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